Next-gen benchtop genome sequencers are here from the three major sequencing vendors Illumina, Ion Torrent (Life Technologies), and Roche. Illumina has MiSeq, Life Technologies has Ion Torrent PGM, and Roche has 454 GS Junior. These benchtop genome sequencers promise to bring the sequencing to individual labs by cutting down the size and the cost.
But, one of the biggest questions that comes to mind is which is the best benchtop high-throughput sequencer. Is it Illumina’s MiSeq, or Ion Torrent’s PGM, or Roche’s 454 GS Junior?.
A UK based research team tried to address the question and compared these benchtop high-throughput sequencers and published their results in the Journal Nature Biotechnology in the article titled “Performance comparison of benchtop high-throughput sequencing platforms.
The team sequenced E.Coli 0104:H4, the strain that caused food poisoning outbreak in Germany in 2011 using Illumina MiSeq, 454 GS Junior Roche, and Ion Torrent PGM.
Well, the answer to the question of best desktop sequencer is not straight forward. As one might have expected, it depends on what one wants to do with the sequencer. But the study has comeup with interesting numbers to compare and help decide. Here is a quick summary of their detailed study comparing the benchtop sequencers.
MiSeq for More Data
Illumina’s MiSeq has the highest throughput of data per run. Ilumina’s Miseq generates 1.6 Giga bases of data per run at the rate of 60 Mb per hour. 454 GS Junior has lowest throughput of data and it produces about 70 Mb per run at the rate of 9Mb per hour. Ion Torrent PGM generates about 300Mb of data per run and it can give the highest throughput of 80-100 Mb per hour when run in 100-bp reads mode.
454 GS Junior for Long Reads
Although 454 GS Junior lost out in the throughput, it won in the longest reads. 454 GS Junior generates reads of length about 500 bases on average and up to 600 bases. Illumina’s MiSeq produces reads of length 150 bases and Ion Torrent PGM is at the third position with read lengths of about 120 bases.
MiSeq for High Quality
The reads from Illumina’s MiSeq were of the highest quality with lowest substitution error rate of 0.1 substitutions per 100 base. When checked for indels after aligning the reads to the reference genome, Ion Torrent PGM had 1.5 indels per every 100 bases and 454 GS Junior had 0.38 indels per 100 bases. A run of identical bases seem to have been the cause of these indels in the Ion Torrent PGM data.
On the otherhand, Illumina’s MiSeq did not have any noticeable indel problems. Illumina’s Miseq produced indels very infrequently at the rate of <0.001 indels per 100 bases.
What about the cost of these benchtop high-throuput sequncers? Without considering service contract costs and the cost of library preps, Illumina’s MiSeq cost the highest with $125,000, closely followed by 454GS Junior costing $108,000 and Ion Torrent PGM costs about $81,000.